Rigify moves twice as far as mesh?
looks like your helpers are children are of the rig and are therefore also affected, my understanding is they should remain static since their referenced by bones. With only your last layer visible go to your outliner, set to only visible layers, select any mesh withing the rig heirarchy, now change your outliner view to same types, select all (A),right click the mesh and chose 'select', hit alt+P in the 3D view to un-parent. Now go back to your first layer and the rig should behave properly.